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- PDB-35tm: Structure of RyDEP-3'cADPR complex in post-reaction state -

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Basic information

Entry
Database: PDB / ID: 35tm
TitleStructure of RyDEP-3'cADPR complex in post-reaction state
ComponentsRyanodine receptor Ryr domain-containing protein
KeywordsVIRAL PROTEIN / immune evasion / viral glycosidase
Function / homologyRyanodine receptor Ryr / RyR domain / Chem-AR6 / Ryanodine receptor Ryr domain-containing protein
Function and homology information
Biological speciesMycobacterium phage DyoEdafos (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLopez Rivera, M. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
Citation
Journal: Biorxiv / Year: 2026
Title: Phage RyR-domain proteins degrade ADPR-based immune signals and fuel NAD + synthesis.
Authors: Lopez Rivera, M. / Chang, R.B. / Lewis, C.M. / Hadary, R. / Kovalski, J.M. / Freeman, K.G. / Sun, Z.J. / Sorek, R. / Hatfull, G.F. / Kranzusch, P.J.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor Ryr domain-containing protein
B: Ryanodine receptor Ryr domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3594
Polymers32,2402
Non-polymers1,1192
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-30 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.825, 67.199, 68.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ryanodine receptor Ryr domain-containing protein


Mass: 16120.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium phage DyoEdafos (virus) / Gene: 78, SEA_DYOEDAFOS_78 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5J6TI87
#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M KSCN, 20% (w/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97905 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.65→68.3 Å / Num. obs: 34402 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 0.998 / Net I/σ(I): 8
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1680 / CC1/2: 0.788

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
RAPDdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→47.9 Å / SU ML: 0.1968 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 1738 5.08 %
Rwork0.1832 32505 -
obs0.185 34243 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.31 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 72 358 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01432410
X-RAY DIFFRACTIONf_angle_d1.33773306
X-RAY DIFFRACTIONf_chiral_restr0.0673338
X-RAY DIFFRACTIONf_plane_restr0.0103416
X-RAY DIFFRACTIONf_dihedral_angle_d15.7634874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.3191270.29742677X-RAY DIFFRACTION99.72
1.7-1.750.29341020.28342708X-RAY DIFFRACTION99.75
1.75-1.820.30541630.25932652X-RAY DIFFRACTION99.68
1.82-1.890.27731440.24122678X-RAY DIFFRACTION99.51
1.89-1.970.29841400.21482663X-RAY DIFFRACTION99.54
1.97-2.080.22321420.19192688X-RAY DIFFRACTION99.58
2.08-2.210.20951650.17272660X-RAY DIFFRACTION99.82
2.21-2.380.24081360.17462717X-RAY DIFFRACTION99.58
2.38-2.620.21551770.16862677X-RAY DIFFRACTION99.65
2.62-30.21641450.16412727X-RAY DIFFRACTION99.83
3-3.780.20331560.1562769X-RAY DIFFRACTION99.9
3.78-47.90.15651410.16032889X-RAY DIFFRACTION99.54
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.732986771690.575142487816-0.6146251276391.496855884660.4734663298841.810360241190.0508893270563-0.08732265772870.240280247309-0.0461834056124-0.05396830611930.0499698787154-0.294320949332-0.0923239193532-0.01112326035140.217131868191-0.00324673899329-0.03982563497020.1987916011070.0143875015760.184068403995-2.0509374187711.8364792796-9.71450518669
21.417076436840.165580294175-0.3341349898940.6171843873580.388863184231.1118458336-0.00269053518911-0.102027552380.1422808582160.0642434948825-0.06104962387430.0819313509961-0.165863583597-0.0187386363890.09007544272660.159285226544-0.0128625430935-0.005308230690310.178905607561-0.001334815865130.136297692428-2.995367729434.0622449519-8.6165551208
37.51217159049-1.15540480583-0.2843984865383.936365948690.3831028883312.681733224120.07638337881970.1234984395640.401006264598-0.1655991530790.0369150127061-0.0071266782829-0.2492796479180.080068359526-0.08570765591010.174943595972-0.02604980400070.01177026820230.1265339136660.02373097163430.1166921811961.207607279639.99926632568-15.5393322088
42.217607208020.120785797196-0.8240863513881.27586026785-0.3444067882361.91382016467-0.0267125181970.1693658822370.10286346176-0.0507126717648-0.00830772166430.0038876183842-0.00533353129735-0.1047684363850.03163374045550.127072866967-0.0193151816967-0.02320178910270.169808758177-0.01269188538650.115982600846-0.0586200351857-0.601809417233-22.2877002567
55.615188741361.76322900143-3.941736216941.44350354654-1.434640933665.44063488303-0.07511810166120.05617065653790.00995226357565-0.07563729395070.01135580417940.05333318909030.153412436543-0.06318939435860.07381758445370.133203541554-0.0332201636571-0.0177493604610.0858991035866-0.01061134679130.1063208863-3.01278613762-4.64464609791-6.95932149544
65.34776778274-2.50812706208-1.073496083581.766206426770.3823823391561.909526503330.017953630069-0.6096616779030.4464164602520.2109328459410.09823712323560.00498755939833-0.101389448632-0.0218545113234-0.2487300249850.210973511374-0.0444779510279-0.004699671259780.14145713618-0.01534637767350.2313909604051.9458978989811.8305822122.78705875803
71.88155307943-0.383284612214-0.5166542432480.357399132207-0.08142936151521.18501896413-0.03168148436960.009126245551210.122168118712-0.00729341667919-0.01351327688420.0481194749354-0.0591567159811-0.0389344703555-0.01850434660520.166817266429-0.0239225160518-0.003064025135330.140813910683-0.01446270175910.1517694126123.014368248254.023968196921.66947010339
84.056297702010.425203925442-0.2236951486821.90030090030.1435485523772.34188331732-0.0727233750752-0.1729371845270.2693420462260.01323620336940.02872579603260.0767485211108-0.2108332827830.0351143401574-0.04170372479120.167757517379-0.01403401057710.004353039613180.1571308545460.006971820897190.136462567591-1.199208718749.948678547028.59895380303
92.14000304967-0.0508147566633-0.9080857679550.252870592172-0.008061712018971.62271073363-0.0108145177423-0.169023135024-0.04993111879680.0547936563636-0.01779510221210.01230562400010.0639738284712-0.002082518335270.01874437143130.164313837618-0.0148480209452-0.01460036358780.1852906860360.02758564358190.1647383055260.074995088053-0.73431983636915.2890704187
107.29462186743-1.56030629813-4.260893457261.309273373121.086418428074.4467763763-0.0761159992217-0.2020870576730.005342525860640.005319953283810.0722873421570.01574717869580.2091942970020.1660104332830.0948152141420.163447434671-0.0262256891959-0.03101253606990.1256452013140.005369068057950.1261057312692.98792490639-4.65473092871-0.036021284529
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 15 )AA0 - 151 - 16
22chain 'A' and (resid 16 through 35 )AA16 - 3517 - 36
33chain 'A' and (resid 36 through 48 )AA36 - 4837 - 49
44chain 'A' and (resid 49 through 110 )AA49 - 11050 - 111
55chain 'A' and (resid 111 through 137 )AA111 - 137112 - 138
66chain 'B' and (resid 0 through 15 )BC0 - 151 - 16
77chain 'B' and (resid 16 through 35 )BC16 - 3517 - 36
88chain 'B' and (resid 36 through 48 )BC36 - 4837 - 49
99chain 'B' and (resid 49 through 110 )BC49 - 11050 - 111
1010chain 'B' and (resid 111 through 137 )BC111 - 137112 - 138

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